Exploring the landscape of focal amplifications in cancer using AmpliconArchitect von Deshpande, Viraj, Luebeck, Jens, Nguyen, Nam-Phuong D., Bakhtiari, Mehrdad, Turner, Kristen M., Schwab, Richard, Carter, Hannah, Mischel, Paul S., Bafna, Vineet

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AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications von Luebeck, Jens, Coruh, Ceyda, Dehkordi, Siavash R., Lange, Joshua T., Turner, Kristen M., Deshpande, Viraj, Pai, Dave A., Zhang, Chao, Rajkumar, Utkrisht, Law, Julie A., Mischel, Paul S., Bafna, Vineet

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ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions von Dolzhenko, Egor, Deshpande, Viraj, Schlesinger, Felix, Krusche, Peter, Petrovski, Roman, Chen, Sai, Emig-Agius, Dorothea, Gross, Andrew, Narzisi, Giuseppe, Bowman, Brett, Scheffler, Konrad, van Vugt, Joke J F A, French, Courtney, Sanchis-Juan, Alba, Ibáñez, Kristina, Tucci, Arianna, Lajoie, Bryan R, Veldink, Jan H, Raymond, F Lucy, Taft, Ryan J, Bentley, David R, Eberle, Michael A

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Staircase detection for safe mobility of visually impaired people von Madake, Jyoti, Bhatlawande, Shripad, Shilaskar, Swati, Deshpande, Piyush, Deshpande, Viraj

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ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer von Nguyen, Nam-phuong D, Deshpande, Viraj, Luebeck, Jens, Mischel, Paul S, Bafna, Vineet

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EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA von Rajkumar, Utkrisht, Turner, Kristen, Luebeck, Jens, Deshpande, Viraj, Chandraker, Manmohan, Mischel, Paul, Bafna, Vineet

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REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats von Dolzhenko, Egor, Weisburd, Ben, Ibañez, Kristina, Rajan-Babu, Indhu-Shree, Anyansi, Christine, Bennett, Mark F, Billingsley, Kimberley, Carroll, Ashley, Clamons, Samuel, Danzi, Matt C, Deshpande, Viraj, Ding, Jinhui, Fazal, Sarah, Halman, Andreas, Jadhav, Bharati, Qiu, Yunjiang, Richmond, Phillip A, Saunders, Christopher T, Scheffler, Konrad, van Vugt, Joke J F A, Zwamborn, Ramona R A J, Chong, Samuel S, Friedman, Jan M, Tucci, Arianna, Rehm, Heidi L, Eberle, Michael A

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Comparison of Arthrofibrosis After ACL Reconstruction According to Graft Choice: Quadriceps Tendon Versus Bone-Patellar Tendon-Bone Autograft von Johnson, Bailey E., Smith, Chelsea L., Smith, Cory D., Quilligan, Edward J., Deshpande, Viraj A., Gardner, Vance O., Parvaresh, Kevin C., Shepard, Michael F., Petrie, Russell S., Prietto, Carlos A., Grumet, Robert C., Gazzaniga, David S.

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Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers von Kim, Hoon, Nguyen, Nam-Phuong, Turner, Kristen, Wu, Sihan, Gujar, Amit D., Luebeck, Jens, Liu, Jihe, Deshpande, Viraj, Rajkumar, Utkrisht, Namburi, Sandeep, Amin, Samirkumar B., Yi, Eunhee, Menghi, Francesca, Schulte, Johannes H., Henssen, Anton G., Chang, Howard Y., Beck, Christine R., Mischel, Paul S., Bafna, Vineet, Verhaak, Roel G. W.

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Preoperative corticosteroid injections are associated with a higher periprosthetic infection rate following primary total shoulder arthroplasty: a systematic review and meta-analys... von Schoell, Kyle, Crabb, Rocio, Simpson, Evan, Deshpande, Viraj, Gardner, Vance, Quilligan, Edward, Parvaresh, Kevin, Kassam, Hafiz

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Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity von Turner, Kristen M., Deshpande, Viraj, Beyter, Doruk, Koga, Tomoyuki, Rusert, Jessica, Lee, Catherine, Li, Bin, Arden, Karen, Ren, Bing, Nathanson, David A., Kornblum, Harley I., Taylor, Michael D., Kaushal, Sharmeela, Cavenee, Webster K., Wechsler-Reya, Robert, Furnari, Frank B., Vandenberg, Scott R., Rao, P. Nagesh, Wahl, Geoffrey M., Bafna, Vineet, Mischel, Paul S.

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Cost-utility of lumbar interbody fusion surgery: A systematic review von Deshpande, Viraj, Simpson, Evan, Caballero, Jesse, Haddad, Chris, Smith, Jeremy, Gardner, Vance

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Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study von Ibañez, Kristina, Polke, James, Hagelstrom, R Tanner, Dolzhenko, Egor, Pasko, Dorota, Thomas, Ellen Rachel Amy, Smith, Katherine R, McDonagh, Ellen M, Polychronopoulos, Dimitris, Chan, Georgia, Davison, James E, Festenstein, Richard, Fratta, Pietro, Giunti, Paola, Howard, Robin, Venkata, Laxmi, Laurá, Matilde, Morris, Huw, Robinson, Robert, Rosser, Elisabeth, Faravelli, Francesca, Schrag, Anette, Schott, Jonathan M, Wood, Nicholas W, Bourn, David, Eggleton, Kelly, Twiss, Philip, Almheiri, Ghareesa, Sheikh, Isabella, Vandrovcova, Jana, Brittain, Helen, Baple, Emma, Moutsianas, Loukas, Deshpande, Viraj, Perry, Denise L, Ajay, Subramanian S., Rajan, Vani, Oprych, Kathryn, Chinnery, Patrick F, Wilson, Gill, Ellard, Sian, Temple, I Karen, McMullan, Dom, Naresh, Kikkeri, Flinter, Frances A, Taylor, Jenny C, Greenhalgh, Lynn, Newman, William, Brennan, Paul, Sayer, John A, Raymond, F Lucy, Deans, Zandra C, Hill, Sue, Fowler, Tom, Scott, Richard H, Chinnery, Patrick F, Rendon, Augusto, Eberle, Michael A, Taft, Ryan J, Arumugam, Prabhu, Bleda, Marta, Boardman-Pretty, Freya, Boissiere, Jeanne M., Devereau, Andrew, Elgar, Greg, Foulger, Rebecca E., Furió-Tarí, Pedro, Hackett, Joanne, Hamblin, Angela, Holman, James, Hubbard, Tim J.P., Jones, Louise J., Kayikci, Melis, Lawson, Kay, Leigh, Sarah E.A., Leong, Ivonne U.S., Maleady-Crowe, Fiona, Mason, Joanne, Mueller, Michael, Murugaesu, Nirupa, Odhams, Chris A., Perez-Gil, Daniel, Pullinger, John, Rahim, Tahrima, Riesgo-Ferreiro, Pablo, Ryten, Mina, Savage, Kevin, Sawant, Kushmita, Sieghart, Alexander, Smedley, Damian, Sosinsky, Alona, Spooner, William, Stevens, Helen E., Stuckey, Alexander, Sultana, Razvan, Tregidgo, Carolyn, Walsh, Emma, Watters, Sarah A., Williams, Eleanor, Zarowiecki, Magdalena

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Revision reverse shoulder arthroplasty: Current concepts for the glenoid von Mathur, Abhay, Deshpande, Viraj, Intarachumnun, Napat, Saunders, Patrick, Kassam, Hafiz F.

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High in-hospital preoperative anxiety levels are not associated with an increased length of stay or readmission following primary shoulder arthroplasty von Crabb, Rocio A.L., Deshpande, Viraj, Urquiza, Noemi, Schoell, Kyle, Guerrero, Sean, Quilligan, Edward J., Kassam, Hafiz F.

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13. AmpliconSuite: Analyzing focal amplifications in cancer genomes von Luebeck, Jens, Huang, Edwin, Dameracharla, Bhargavi, Kim, Forrest, Liefeld, Ted, Ahuja, Rohil, Prasad, Daniel Schreyer, Prasad, Gino, Kim, Soyeon, Kim, Hoon, Bailey, Peter, Verhaak, Roel, Deshpande, Viraj, Reich, Michael, Mischel, Paul, Mesirov, Jill, Bafna, Vineet

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Additional file 3 of REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats von Dolzhenko, Egor, Weisburd, Ben, Ibañez, Kristina, Rajan-Babu, Indhu-Shree, Anyansi, Christine, Bennett, Mark F., Billingsley, Kimberley, Carroll, Ashley, Clamons, Samuel, Danzi, Matt C., Deshpande, Viraj, Ding, Jinhui, Fazal, Sarah, Halman, Andreas, Jadhav, Bharati, Qiu, Yunjiang, Richmond, Phillip A., Saunders, Christopher T., Scheffler, Konrad, van Vugt, Joke J. F. A., Zwamborn, Ramona R. A. J., Chong, Samuel S., Friedman, Jan M., Tucci, Arianna, Rehm, Heidi L., Eberle, Michael A.

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Cerulean: A Hybrid Assembly Using High Throughput Short and Long Reads von Deshpande, Viraj, Fung, Eric D. K., Pham, Son, Bafna, Vineet

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AmpliconArchitect_reconstructions von Viraj Deshpande

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RAPID DETECTION OF GENE FUSIONS von RODDEY, John Cooper, CATREUX, Severine, MEHIO, Rami, TRUONG, Sean, SCHLESINGER, Johann Felix Wilhelm, DESHPANDE, Viraj, RUEHLE, Michael

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